Module frame_order

The automated frame order analysis protocol.

Usage

To use this analysis, you should import the following into your script:

• Frame_order_analysis: This is a Python class which contains the automated protocol. Initialising the class will execute the full analysis. See its documentation for all the options it accepts.
• Optimisation_settings: This is a Python class which is used to set up and store the optimisation settings used in the automated protocol. This allows for grid searches, zooming grid searches, minimisation settings, quasi-random Sobol' numerical integration of the PCS, and SciPy quadratic numerical integration of the PCS to be specified.

See the sample scripts for examples of how these are used. In addition, the following two functions provide summaries of the analysis:

• count_sobol_points: This function will summarize the number of quasi-random Sobol' points used in the PCS numeric integration. The table it creates is very useful for judging the quality of the current optimisation settings.
• summarise: This function will summarise all of the current frame order results.

Both these functions will be called at the end of the auto-analysis. However they can also be used in simple scripts to summarise the results as an analysis is progressing.

The nested model parameter copying protocol

To allow the analysis to complete in under 1,000,000 years, the trick of copying parameters from simpler nested models is used in this auto-analysis. The protocol is split into four categories for the average domain position, the pivot point, the motional eigenframe and the parameters of ordering. These use the fact that the free rotor and torsionless models are the two extrema of the models where the torsion angle is restricted, whereby sigma_max is pi and 0 respectively.

Classes

Frame_order_analysis
The frame order auto-analysis protocol.

Optimisation_settings
A special object for storing the settings for optimisation.

Functions

count_sobol_points(file_name='sobol_point_count', dir=None, force=True)
Count the number of Sobol' points used for the PCS numerical integration.

model_directory(model, base_dir=None)
Return the directory to be used for the model.

summarise(file_name='summary', dir=None, force=True)
Summarise the frame order auto-analysis results.

Variables

ds = The relax data storage obje...

status = Status()

__package__ = 'auto_analyses'

Imports: pi, float64, zeros, F_OK, access, getcwd, sep, sys, Relax_data_store, is_bool, is_float, is_int, is_str, RelaxError, convert_axis_alpha_to_spherical, MODEL_DOUBLE_ROTOR, MODEL_FREE_ROTOR, MODEL_ISO_CONE, MODEL_ISO_CONE_FREE_ROTOR, MODEL_ISO_CONE_TORSIONLESS, MODEL_LIST, MODEL_LIST_FREE_ROTORS, MODEL_LIST_ISO_CONE, MODEL_LIST_NONREDUNDANT, MODEL_LIST_PSEUDO_ELLIPSE, MODEL_PSEUDO_ELLIPSE, MODEL_PSEUDO_ELLIPSE_FREE_ROTOR, MODEL_PSEUDO_ELLIPSE_TORSIONLESS, MODEL_RIGID, MODEL_ROTOR, wrap_angles, spherical_to_cartesian, open_write_file, subtitle, subsubtitle, title, MULTI_COL, format_table, pipes, results, return_spin, spin_loop, pipe_centre_of_mass, Interpreter, generate_pivot, optimisation, Status

Function Details

count_sobol_points(file_name='sobol_point_count', dir=None, force=True)

Count the number of Sobol' points used for the PCS numerical integration.

This function can be used while a frame order analysis is running to summarise the results. It will create a table of the number of Sobol' points used, which can then be used to judge the quality of the integration.

Parameters:

• file_name (str) - The file to save the table into.
• dir (None or str) - The optional directory to place the file into. If specified, the results files will also be searched for in this directory.
• force (bool) - A flag which if True will cause any preexisting file to be overwritten.

model_directory(model, base_dir=None)

Return the directory to be used for the model.

Parameters:

• model (str) - The frame order model name.
• base_dir (None or str) - The optional base directory to prepend to the file name.

summarise(file_name='summary', dir=None, force=True)

Summarise the frame order auto-analysis results.

This function can be used while a frame order analysis is running to summarise the results. It will create a table of the statistics and model parameters for all of the optimised frame order models for which results files currently exist.

Parameters:

• file_name (str) - The file to save the table into.
• dir (None or str) - The optional directory to place the file into. If specified, the results files will also be searched for in this directory.
• force (bool) - A flag which if True will cause any preexisting file to be overwritten.

Variables Details

ds

Value:

The relax data storage object.

Data pipes:
  None

Data store objects:
  __dict__ <type 'dict'>: dict() -> new empty dictionary
  __doc__ <type 'str'>: The relax data storage object.
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